1
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Lin CJ, Siddique S. Parasitic nematodes: dietary habits and their implications. Trends Parasitol 2024; 40:230-240. [PMID: 38262837 DOI: 10.1016/j.pt.2023.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/25/2023] [Accepted: 12/27/2023] [Indexed: 01/25/2024]
Abstract
Nematodes, a diverse group of roundworms, exhibit a wide range of dietary habits, including parasitism of animals and plants. These parasites cause substantial economic losses in agriculture and pose significant health challenges to humans and animals. This review explores the unique adaptations of parasitic nematodes, emphasizing their nutritional requirements and metabolic dependencies. Recent research has identified cross-kingdom compartmentalization of vitamin B5 biosynthesis in some parasitic nematodes, shedding light on coevolutionary dynamics and potential targets for control strategies. Several open questions remain regarding the complexity of nematode nutrition, host manipulation, evolutionary adaptations, and the influence of environmental factors on their metabolic processes. Understanding these aspects offers promising avenues for targeted interventions to manage and control these economically and medically important parasites.
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Affiliation(s)
- Ching-Jung Lin
- Department of Plant Pathology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Shahid Siddique
- Department of Entomology and Nematology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA.
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2
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Wolstenholme AJ, Andersen EC, Choudhary S, Ebner F, Hartmann S, Holden-Dye L, Kashyap SS, Krücken J, Martin RJ, Midha A, Nejsum P, Neveu C, Robertson AP, von Samson-Himmelstjerna G, Walker R, Wang J, Whitehead BJ, Williams PDE. Getting around the roundworms: Identifying knowledge gaps and research priorities for the ascarids. ADVANCES IN PARASITOLOGY 2024; 123:51-123. [PMID: 38448148 PMCID: PMC11143470 DOI: 10.1016/bs.apar.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
The ascarids are a large group of parasitic nematodes that infect a wide range of animal species. In humans, they cause neglected diseases of poverty; many animal parasites also cause zoonotic infections in people. Control measures include hygiene and anthelmintic treatments, but they are not always appropriate or effective and this creates a continuing need to search for better ways to reduce the human, welfare and economic costs of these infections. To this end, Le Studium Institute of Advanced Studies organized a two-day conference to identify major gaps in our understanding of ascarid parasites with a view to setting research priorities that would allow for improved control. The participants identified several key areas for future focus, comprising of advances in genomic analysis and the use of model organisms, especially Caenorhabditis elegans, a more thorough appreciation of the complexity of host-parasite (and parasite-parasite) communications, a search for novel anthelmintic drugs and the development of effective vaccines. The participants agreed to try and maintain informal links in the future that could form the basis for collaborative projects, and to co-operate to organize future meetings and workshops to promote ascarid research.
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Affiliation(s)
- Adrian J Wolstenholme
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Université de Tours, ISP, Nouzilly, France.
| | - Erik C Andersen
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
| | - Shivani Choudhary
- Department of Biomedical Sciences, Iowa State University, Ames, IA, United States
| | - Friederike Ebner
- Department of Molecular Life Sciences, School of Life Sciences, Technische Universität München, Freising, Germany
| | - Susanne Hartmann
- Institute for Immunology, Freie Universität Berlin, Berlin, Germany
| | - Lindy Holden-Dye
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Sudhanva S Kashyap
- Department of Biomedical Sciences, Iowa State University, Ames, IA, United States
| | - Jürgen Krücken
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Richard J Martin
- Department of Biomedical Sciences, Iowa State University, Ames, IA, United States
| | - Ankur Midha
- Institute for Immunology, Freie Universität Berlin, Berlin, Germany
| | - Peter Nejsum
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Cedric Neveu
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Université de Tours, ISP, Nouzilly, France
| | - Alan P Robertson
- Department of Biomedical Sciences, Iowa State University, Ames, IA, United States
| | | | - Robert Walker
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Jianbin Wang
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, United States
| | | | - Paul D E Williams
- Department of Biomedical Sciences, Iowa State University, Ames, IA, United States
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3
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Zheng Y, Young ND, Song J, Gasser RB. Genome-Wide Analysis of Haemonchus contortus Proteases and Protease Inhibitors Using Advanced Informatics Provides Insights into Parasite Biology and Host-Parasite Interactions. Int J Mol Sci 2023; 24:12320. [PMID: 37569696 PMCID: PMC10418638 DOI: 10.3390/ijms241512320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
Biodiversity within the animal kingdom is associated with extensive molecular diversity. The expansion of genomic, transcriptomic and proteomic data sets for invertebrate groups and species with unique biological traits necessitates reliable in silico tools for the accurate identification and annotation of molecules and molecular groups. However, conventional tools are inadequate for lesser-known organismal groups, such as eukaryotic pathogens (parasites), so that improved approaches are urgently needed. Here, we established a combined sequence- and structure-based workflow system to harness well-curated publicly available data sets and resources to identify, classify and annotate proteases and protease inhibitors of a highly pathogenic parasitic roundworm (nematode) of global relevance, called Haemonchus contortus (barber's pole worm). This workflow performed markedly better than conventional, sequence-based classification and annotation alone and allowed the first genome-wide characterisation of protease and protease inhibitor genes and gene products in this worm. In total, we identified 790 genes encoding 860 proteases and protease inhibitors representing 83 gene families. The proteins inferred included 280 metallo-, 145 cysteine, 142 serine, 121 aspartic and 81 "mixed" proteases as well as 91 protease inhibitors, all of which had marked physicochemical diversity and inferred involvements in >400 biological processes or pathways. A detailed investigation revealed a remarkable expansion of some protease or inhibitor gene families, which are likely linked to parasitism (e.g., host-parasite interactions, immunomodulation and blood-feeding) and exhibit stage- or sex-specific transcription profiles. This investigation provides a solid foundation for detailed explorations of the structures and functions of proteases and protease inhibitors of H. contortus and related nematodes, and it could assist in the discovery of new drug or vaccine targets against infections or diseases.
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Affiliation(s)
- Yuanting Zheng
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia;
| | - Neil D. Young
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia;
| | - Jiangning Song
- Department of Data Science and AI, Faculty of IT, Monash University, Melbourne, VIC 3800, Australia;
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
- Monash Data Futures Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Robin B. Gasser
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia;
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4
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Williams PDE, Kashyap SS, McHugh MA, Brewer MT, Robertson AP, Martin RJ. Diethylcarbamazine, TRP channels and Ca 2+ signaling in cells of the Ascaris intestine. Sci Rep 2022; 12:21317. [PMID: 36494409 PMCID: PMC9734116 DOI: 10.1038/s41598-022-25648-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
The nematode parasite intestine absorbs nutrients, is involved in innate immunity, can metabolize xenobiotics and as we show here, is also a site of action of the anthelmintic, diethylcarbamazine. Diethylcarbamazine (DEC) is used to treat lymphatic filariasis and activates TRP-2, GON-2 & CED-11 TRP channels in Brugia malayi muscle cells producing spastic paralysis. DEC also has stimulatory effects on ascarid nematode parasites. Using PCR techniques, we detected, in Ascaris suum intestine, message for: Asu-trp-2, Asu-gon-2, Asu-ced-11, Asu-ocr-1, Asu-osm-9 and Asu-trpa-1. Comparison of amino-acid sequences of the TRP channels of B. malayi, and A. suum revealed noteworthy similarity, suggesting that the intestine of Ascaris will also be sensitive to DEC. We used Fluo-3AM as a Ca2+ indicator and observed characteristic unsteady time-dependent increases in the Ca2+ signal in the intestine in response to DEC. Application of La3+ and the TRP channel inhibitors, 2-APB or SKF 96365, inhibited DEC mediated increases in intracellular Ca2+. These observations are important because they emphasize that the nematode intestine, in addition to muscle, is a site of action of DEC as well as other anthelmintics. DEC may also enhance the Ca2+ toxicity effects of other anthelmintics acting on the intestine or, increase the effects of other anthelmintics that are metabolized and excreted by the nematode intestine.
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Affiliation(s)
- Paul D E Williams
- Department of Biomedical Sciences, Iowa State University, Ames, IA, USA
| | | | - Mark A McHugh
- Department of Biomedical Sciences, Iowa State University, Ames, IA, USA
| | - Matthew T Brewer
- Department of Veterinary Pathology, Iowa State University, Ames, IA, USA
| | - Alan P Robertson
- Department of Biomedical Sciences, Iowa State University, Ames, IA, USA
| | - Richard J Martin
- Department of Biomedical Sciences, Iowa State University, Ames, IA, USA.
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5
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Dahal S, Gour P, Raghuvanshi S, Prasad YK, Saikia D, Ghatani S. Multi-stage transcriptome profiling of the neglected food-borne echinostome Artyfechinostomum sufrartyfex reveal potential diagnostic and drug targets. Acta Trop 2022; 233:106564. [PMID: 35716764 DOI: 10.1016/j.actatropica.2022.106564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 06/01/2022] [Accepted: 06/09/2022] [Indexed: 11/28/2022]
Abstract
Lack of effective surveillance and control methods for neglected helminth diseases particularly in context of rural areas in India is a serious concern in terms of public health. With regard to the emerging food-borne echinostomid Artyfechinostomum sufrartyfex infection in the country, the current study is an in silico attempt to screen for plausible diagnostic and drug targets against the trematode. Transcriptome of adult, encysted and excysted metacercaria stages of the parasite was generated using Illumina sequencing platform. A de-novo assembly strategy utilizing transcriptome data generated from the three lifecycle stages was followed to generate the representative transcripts. Longest open reading frames identified for the transcripts were further conceptually translated into their respective protein sequences. Detailed analysis of this dataset through various bioinformatics pipelines and tools eventually identified 14 credible diagnostic and 10 drug targets along with their FDA-approved and ZINC molecules. Some of the important diagnostic candidates include thioredoxin peroxidase, haemoglobinase, cathepsin L, cathepsin L-like and B-like cysteine proteases. Among the drug targets, uncharacterized sodium dependent transporter and bifunctional protein Aas were identified as top targets exhibiting significant interaction with Rifamycin and ZINC02820058 molecule, respectively. Further, B-cell epitope analysis of the diagnostic targets revealed unique epitopes for 10 of them thus indicating their potential role in specific diagnosis of the parasite. The diagnostic candidates along with a number of lesser known drug targets and their ligand molecules identified in this study provides a reasonable basis for evaluation and development of future intervention strategies against A. sufrartyfex.
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Affiliation(s)
- Suman Dahal
- Department of Zoology, School of Life sciences, Sikkim University, Gangtok, Sikkim, India
| | - Pratibha Gour
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | | | - Dipshikha Saikia
- Department of Zoology, School of Life sciences, Sikkim University, Gangtok, Sikkim, India
| | - Sudeep Ghatani
- Department of Zoology, School of Life sciences, Sikkim University, Gangtok, Sikkim, India.
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6
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Wang C, Gao W, Yan S, Zhu XQ, Suo X, Liu X, Gupta N, Hu M. N-glycome and N-glycoproteome of a hematophagous parasitic nematode Haemonchus. Comput Struct Biotechnol J 2021; 19:2486-2496. [PMID: 34025939 PMCID: PMC8113779 DOI: 10.1016/j.csbj.2021.04.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 12/24/2022] Open
Abstract
N-glycosylation is a physiologically vital post-translational modification of proteins in eukaryotic organisms. Initial work on Haemonchus contortus - a blood-sucking nematode of ruminants with a broad geographical distribution - has shown that this parasite harbors N-glycans with exclusive chitobiose modifications. Besides, several immunogenic proteins (e.g., amino- and metallo-peptidases) are known to be N-glycosylated in adult worms. However, an informative atlas of N-glycosylation in H. contortus is not yet available. Herein, we report 291 N-glycosylated proteins with a total of 425 modification sites in the parasite. Among them, many peptidase families (e.g., peptidase C1 and M1) including potential vaccine targets were enriched. Notably, the glycan-rich conjugates are distributed primarily in the intestine and gonads of adult worms, and consequently hidden from the host's immune system. Collectively, these data provide a comprehensive atlas of N-glycosylation in a prevalent parasitic nematode while underlining its significance for infection, immunity and prevention.
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Key Words
- Con A, concanavalin A
- Fuc, fucose
- Gal, galactose
- Gal-Fuc, galactosylated fucose
- GalNAc, N-acetylgalactosamine
- GlcNAc, N-acetylglucosamine
- Glycopeptide
- HILIC, hydrophilic interaction chromatography
- Haemonchus contortus
- LC-MS/MS, liquid chromatography-tandem mass spectrometry
- MALDI-ToF MS, matrix-assisted laser desorption ionization-time of flight mass spectrometry
- Man, mannose
- Mass spectrometry
- N-glycan
- N-glycosylation
- OST, oligosaccharyltransferase
- PNGase A/F, peptide-N-glycosidase A/F
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Affiliation(s)
- Chunqun Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Wenjie Gao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China,College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Shi Yan
- Institut für Parasitologie, Veterinärmedizinische Universität, Wien, Austria
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xun Suo
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
| | - Xin Liu
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Nishith Gupta
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Department of Molecular Parasitology, Faculty of Life Sciences, Humboldt University, Berlin, Germany,Department of Biological Sciences, Birla Institute of Technology and Science Pilani (BITS-P), Hyderabad, India
| | - Min Hu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Corresponding author at: College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan St., Wuhan, Hubei Province 430070, China.
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7
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Jasmer DP, Rosa BA, Tyagi R, Bulman CA, Beerntsen B, Urban JF, Sakanari J, Mitreva M. De novo identification of toxicants that cause irreparable damage to parasitic nematode intestinal cells. PLoS Negl Trop Dis 2020; 14:e0007942. [PMID: 32453724 PMCID: PMC7274465 DOI: 10.1371/journal.pntd.0007942] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 06/05/2020] [Accepted: 05/04/2020] [Indexed: 02/06/2023] Open
Abstract
Efforts to identify new drugs for therapeutic and preventive treatments against parasitic nematodes have gained increasing interest with expanding pathogen omics databases and drug databases from which new anthelmintic compounds might be identified. Here, a novel approach focused on integrating a pan-Nematoda multi-omics data targeted to a specific nematode organ system (the intestinal tract) with evidence-based filtering and chemogenomic screening was undertaken. Based on de novo computational target prioritization of the 3,564 conserved intestine genes in A. suum, exocytosis was identified as a high priority pathway, and predicted inhibitors of exocytosis were tested using the large roundworm (Ascaris suum larval stages), a filarial worm (Brugia pahangi adult and L3), a whipworm (Trichuris muris adult), and the non-parasitic nematode Caenorhabditis elegans. 10 of 13 inhibitors were found to cause rapid immotility in A. suum L3 larvae, and five inhibitors were effective against the three phylogenetically diverse parasitic nematode species, indicating potential for a broad spectrum anthelmintics. Several distinct pathologic phenotypes were resolved related to molting, motility, or intestinal cell and tissue damage using conventional and novel histologic methods. Pathologic profiles characteristic for each inhibitor will guide future research to uncover mechanisms of the anthelmintic effects and improve on drug designs. This progress firmly validates the focus on intestinal cell biology as a useful resource to develop novel anthelmintic strategies.
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Affiliation(s)
- Douglas P Jasmer
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, United States of America
| | - Bruce A Rosa
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Rahul Tyagi
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Christina A Bulman
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Brenda Beerntsen
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, United States of America
| | - Joseph F Urban
- U.S. Department of Agriculture, Northeast Area, Agricultural Research Service, Beltsville Agricultural Research Center, Animal Parasite Diseases Laboratory and Beltsville Human Nutrition Research Center, Diet Genomics and Immunology Laboratory, Beltsville, Maryland, United States of America
| | - Judy Sakanari
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Makedonka Mitreva
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America.,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
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8
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Torralbo-Ramírez V, Molina-Fernández D, Malagón D, Benítez R, Adroher FJ. Differential Cleaving of Specific Substrates for Cathepsin-Like Activity Shows Cysteine and Serine Protease Activities and a Differential Profile BetweenAnisakis simplex s.s.andAnisakis pegreffii, Sibling Species Major Etiologic Agents of Anisakiasis. Foodborne Pathog Dis 2019; 16:744-751. [DOI: 10.1089/fpd.2019.2633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
| | | | - David Malagón
- Departamento de Parasitología, Facultad de Farmacia, Universidad de Granada, Granada, Spain
| | - Rocío Benítez
- Departamento de Parasitología, Facultad de Farmacia, Universidad de Granada, Granada, Spain
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9
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Jasmer DP, Rosa BA, Tyagi R, Mitreva M. Omics Driven Understanding of the Intestines of Parasitic Nematodes. Front Genet 2019; 10:652. [PMID: 31402928 PMCID: PMC6669237 DOI: 10.3389/fgene.2019.00652] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 06/19/2019] [Indexed: 01/25/2023] Open
Abstract
The biological and molecular complexity of nematodes has impeded research on development of new therapies for treatment and control. We have focused on the versatility of the nematode intestine as a target for new therapies. To that end, it is desirable to establish a broad and deep understanding of the molecular architecture underlying intestinal cell functions at the pan-Nematoda level. Multiomics data were generated to uncover the evolutionary principles underlying both conserved and adaptable features of the nematode intestine. Whole genomes were used to reveal the functional potential of the nematodes, tissue-specific transcriptomes provided a deep assessment of genes that are expressed in the adult nematode intestine, and comparison of selected core species was used to determine a first approximation of the pan-Nematoda intestinal transcriptome. Differentially expressed transcripts were also identified among intestinal regions, with the largest number expressed at significantly higher levels in the anterior region, identifying this region as the most functionally unique compared to middle and posterior regions. Profiling intestinal miRNAs targeting these genes identified the conserved intestinal miRNAs. Proteomics of intestinal cell compartments assigned proteins to several different intestinal cell compartments (intestinal tissue, the integral and peripheral intestinal membranes, and the intestinal lumen). Finally, advanced bioinformatic approaches were used to predict intestinal cell functional categories of seminal importance to parasite survival, which can now be experimentally tested and validated. The data provide the most comprehensive compilation of constitutively and differentially expressed genes, predicted gene regulators, and proteins of the nematode intestine. The information provides knowledge that is essential to understand molecular features of nematode intestinal cells and functions of fundamental importance to the intestine of many, if not all, parasitic nematodes.
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Affiliation(s)
- Douglas P Jasmer
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
| | - Bruce A Rosa
- McDonnell Genome Institute, Washington University, St. Louis, St. Louis, MI, United States
| | - Rahul Tyagi
- McDonnell Genome Institute, Washington University, St. Louis, St. Louis, MI, United States
| | - Makedonka Mitreva
- McDonnell Genome Institute, Washington University, St. Louis, St. Louis, MI, United States.,Department of Internal Medicine, Washington University School of Medicine, St. Louis, MI, United States
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10
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Caffrey CR, Goupil L, Rebello KM, Dalton JP, Smith D. Cysteine proteases as digestive enzymes in parasitic helminths. PLoS Negl Trop Dis 2018; 12:e0005840. [PMID: 30138310 PMCID: PMC6107103 DOI: 10.1371/journal.pntd.0005840] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We briefly review cysteine proteases (orthologs of mammalian cathepsins B, L, F, and C) that are expressed in flatworm and nematode parasites. Emphasis is placed on enzyme activities that have been functionally characterized, are associated with the parasite gut, and putatively contribute to degrading host proteins to absorbable nutrients [1–4]. Often, gut proteases are expressed as multigene families, as is the case with Fasciola [5] and Haemonchus [6], presumably expanding the range of substrates that can be degraded, not least during parasite migration through host tissues [5]. The application of the free-living planarian and Caenorhabditis elegans as investigative models for parasite cysteine proteases is discussed. Finally, because of their central nutritive contribution, targeting the component gut proteases with small-molecule chemical inhibitors and understanding their utility as vaccine candidates are active areas of research [7].
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Affiliation(s)
- Conor R. Caffrey
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
| | - Louise Goupil
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
- Department of Biology, University of San Francisco, San Francisco, California, United States of America
| | - Karina M. Rebello
- Laboratório de Toxinologia and Laboratório de Estudos Integrados em Protozoologia, Instituto Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - John P. Dalton
- School of Biological Sciences, Medical Biology Centre, Queen´s University Belfast, Belfast, United Kingdom
| | - David Smith
- School of Biological Sciences, Medical Biology Centre, Queen´s University Belfast, Belfast, United Kingdom
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11
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Rosa BA, McNulty SN, Mitreva M, Jasmer DP. Direct experimental manipulation of intestinal cells in Ascaris suum, with minor influences on the global transcriptome. Int J Parasitol 2017; 47:271-279. [PMID: 28223178 DOI: 10.1016/j.ijpara.2016.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/16/2016] [Accepted: 12/21/2016] [Indexed: 12/24/2022]
Abstract
Ascaris suum provides a powerful model for studying parasitic nematodes, including individual tissues such as the intestine, an established target for anthelmintic treatments. Here, we add a valuable experimental component to our existing functional, proteomic, transcriptomic and phylogenomic studies of the Ascaris suum intestine, by developing a method to manipulate intestinal cell functions via direct delivery of experimental treatments (in this case, double-stranded (ds)RNA) to the apical intestinal membrane. We developed an intestinal perfusion method for direct, controlled delivery of dsRNA/heterogeneous small interfering (hsi) RNA into the intestinal lumen for experimentation. RNA-Seq (22 samples) was used to assess influences of the method on global intestinal gene expression. Successful mRNA-specific knockdown in intestinal cells of adult A. suum was accomplished with this new experimental method. Global transcriptional profiling confirmed that targeted transcripts were knocked down more significantly than any others, with only 12 (0.07% of all genes) or 238 (1.3%) off-target gene transcripts consistently differentially regulated by dsRNA treatment or the perfusion experimental design, respectively (after 24h). The system supports controlled, effective delivery of treatments (dsRNA/hsiRNA) to the apical intestinal membrane with relatively minor off-target effects, and builds on our experimental model to dissect A. suum intestinal cell functions with broad relevance to parasitic nematodes.
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Affiliation(s)
- Bruce A Rosa
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Samantha N McNulty
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Makedonka Mitreva
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Douglas P Jasmer
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164, USA.
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12
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Gao X, Tyagi R, Magrini V, Ly A, Jasmer DP, Mitreva M. Compartmentalization of functions and predicted miRNA regulation among contiguous regions of the nematode intestine. RNA Biol 2016; 14:1335-1352. [PMID: 27002534 DOI: 10.1080/15476286.2016.1166333] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The intestine of parasitic nematodes has proven an important target for therapies aimed at prevention and treatment of diseases caused by these pathogens in humans, animals and plants. We have developed a unique research model with the intestine of Ascaris suum, the large round worm of swine and humans, that will enhance biological research on this tissue. To expand utility of this model, we quantitatively compared expression of 15,382 coding RNAs and 277 noncoding, micro RNAs (miRNAs) among 3 contiguous regions of the adult A. suum intestine. Differentially expressed transcripts were identified among regions, with the largest number expressed at significantly higher levels in the anterior region, identifying this region as the most functionally unique compared to middle and posterior regions. We further identified 64 exon splice variants (from 47 genes) that are differentially expressed among these regions. A total of 2,063 intestinal mRNA transcripts were predicted to be targeted by intestinal miRNA, and negative correlation coefficients for miRNA:mRNA abundances predicted 22 likely influential miRNAs and 503 likely associated miRNA:mRNA pairs. A. suum intestinal miRNAs were identified that are conserved with intestinal miRNAs from C. elegans (10 mature sequences and 13 seed sequences conserved), and prospective intestinal miRNAs from the murine gastrointestinal nematode, Heligmosomoides polygyrus (5 mature and 11 seeds). Most of the conserved intestinal miRNAs were also high abundance miRNAs. The data provide the most comprehensive compilation of constitutively and differentially expressed genes along the length of the intestine for any nematode species. The information will guide prospective development of many hypotheses on nematode intestinal functions encoded by mRNAs, miRNAs and interactions between these RNA populations.
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Affiliation(s)
- Xin Gao
- a McDonnell Genome Institute, Washington University in St. Louis , St. Louis , MO , USA
| | - Rahul Tyagi
- a McDonnell Genome Institute, Washington University in St. Louis , St. Louis , MO , USA
| | - Vincent Magrini
- a McDonnell Genome Institute, Washington University in St. Louis , St. Louis , MO , USA
| | - Amy Ly
- a McDonnell Genome Institute, Washington University in St. Louis , St. Louis , MO , USA
| | - Douglas P Jasmer
- b Department of Veterinary Microbiology and Pathology , Washington State University , Pullman , WA , USA
| | - Makedonka Mitreva
- a McDonnell Genome Institute, Washington University in St. Louis , St. Louis , MO , USA.,c Department of Internal Medicine , Washington University School of Medicine , St. Louis , MO , USA
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Wang Q, Rosa BA, Jasmer DP, Mitreva M. Pan-Nematoda Transcriptomic Elucidation of Essential Intestinal Functions and Therapeutic Targets With Broad Potential. EBioMedicine 2015; 2:1079-89. [PMID: 26501106 PMCID: PMC4587998 DOI: 10.1016/j.ebiom.2015.07.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 07/22/2015] [Accepted: 07/22/2015] [Indexed: 01/22/2023] Open
Abstract
The nematode intestine is continuous with the outside environment, making it easily accessible to anthelmintics for parasite control, but the development of new therapeutics is impeded by limited knowledge of nematode intestinal cell biology. We established the most comprehensive nematode intestinal functional database to date by generating transcriptional data from the dissected intestines of three parasitic nematodes spanning the phylum, and integrating the results with the whole proteomes of 10 nematodes (including 9 pathogens of humans or animals) and 3 host species and 2 outgroup species. We resolved 10,772 predicted nematode intestinal protein families (IntFams), and studied their presence and absence within the different lineages (births and deaths) among nematodes. Conserved intestinal cell functions representing ancestral functions of evolutionary importance were delineated, and molecular features useful for selective therapeutic targeting were identified. Molecular patterns conserved among IntFam proteins demonstrated large potential as therapeutic targets to inhibit intestinal cell functions with broad applications towards treatment and control of parasitic nematodes.
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Affiliation(s)
- Qi Wang
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Bruce A. Rosa
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Douglas P. Jasmer
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, USA
| | - Makedonka Mitreva
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Division of Infectious Disease, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
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